Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 1-alpha.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11500 g11500.t9 TSS g11500.t9 16650082 16650082
chr_1 g11500 g11500.t9 isoform g11500.t9 16650214 16652523
chr_1 g11500 g11500.t9 exon g11500.t9.exon1 16650214 16650931
chr_1 g11500 g11500.t9 cds g11500.t9.CDS1 16650214 16650931
chr_1 g11500 g11500.t9 exon g11500.t9.exon2 16651140 16651594
chr_1 g11500 g11500.t9 cds g11500.t9.CDS2 16651140 16651594
chr_1 g11500 g11500.t9 exon g11500.t9.exon3 16651670 16652523
chr_1 g11500 g11500.t9 cds g11500.t9.CDS3 16651670 16651738
chr_1 g11500 g11500.t9 TTS g11500.t9 16652519 16652519

Sequences

>g11500.t9 Gene=g11500 Length=2027
ATGGGTAAAGAGAAGACTCATATTAATATTGTTGTCATTGGACATGTCGATTCTGGCAAG
TCAACTACAACCGGTCACTTGATCTACAAATGTGGCGGTATTGACAAACGTACCATCGAG
AAGTTCGAGAAGGAAGCTCAAGAAATGGGCAAAGGTTCATTCAAATACGCATGGGTATTG
GATAAGTTGAAGGCTGAACGTGAGCGTGGTATCACCATTGATATCGCCTTATGGAAGTTT
GAAACTGCCAAGTACTACGTTACCATCATTGACGCTCCTGGACATCGTGATTTCATCAAG
AACATGATTACAGGAACATCTCAAGCCGATTGCGCTGTATTGATTGTCGCTGCTGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAGCATGCATTGTTGGCT
TTCACATTGGGTGTTAAGCAATTGATTGTCGGTGTCAACAAGATGGACTCAACTGAGCCA
CCATACTCAGAAGCACGTTTCGAGGAAATTAAAAAGGAAGTCTCGTCATACATCAAGAAG
ATCGGTTATAATCCAGCTGCTGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAGATAAAATGCCATGGTTCAAGGGCTGGGCTATTGAACGCAAAGAA
GGCAAGGCTGATGGCAAATGTCTTATTGATGCTTTGGACGCCATTTTACCACCACAACTA
AAATCAGTCGAAATGCATCATGAAGCTTTGCAAGAAGCTGTACCTGGTGACAATGTTGGT
TTTAACGTCAAGAACGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACAGC
AAGAGCAGTCCACCACGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCAT
CCAGGTCAAATTGCAAATGGTTATACACCAGTTTTGGATTGTCACACTGCTCACATTGCT
TGCAAATTTGCTGAAATCAAAGAGAAGTGCGATCGTCGTACTGGCAAGACAACAGAAGAG
AATCCAAAGGCTATCAAATCAGGTGATGCCGCTATTGTGAATTTAGTTCCATCAAAGCCA
TTGTGTGTTGAATCATTCTCCGAATTTCCACCATTGGGACGTTTTGCTGTTCGTGACATG
AGACAAACTGTTGCTGTTGGTGTTATCAAAGCCGTTAACTTCAAAGAAGCGAGCGGTGGA
AAAGTAACAAAAGCCGCTGAGAAGGCAGCAAAGAAAAAATAACTAGATTGTCAACTTGGC
AAATTTGCCGTGTTTCGATTATCGAACGGCAAACTTGAAATTTTTCATTCTATAAGAAAT
ATTCAAACATTTCACCATGCTGATGGTGTCAAACATCTTTTTCAATTGATTTCTTCTACT
CTTTCTAATAACTTTTATTTTACACATCCCCATTCGTTTTTAATCTTTCATCATCATCGC
AGGAAAAAGCCGAATGGATGTCATTTCTTTTTCGATTTATTCTCATTTACGTTGCATAAG
ATTAATTTAGTTTTGGCAAATGTTGTCAATATTAAGACAAAACAAATAAACTTATGATAA
CATCATTTTATAGTTGCGAGTTTATTTTAATTTTGGCCATACACACACACACAATACACA
GGAATGGAAAAGGATCGAAGGCTATTTCTTTATTTAAATAATAATGATTAGAAGTACCTA
CGTGTATAGTCTTCTTCTTATAATTTGTGATATTTTTTAAGTTGAAGAAATCATTGAGGC
GTTACTTTAAATATTTACTTACTTACTTATTATTGATAAATTAACTCTTCTCTAATAAAC
GAGAACGAAATATTAAATTGGTGAAACTGTAATAGTTTATTACGAATAATTTTTTTGGCT
ATTAAATTGTTACATGCAAGAATAAAAGCGAGACACACAAGAGAAAAAAAAGTTTTGTAT
TGCACCTGTTTCCGATAAATGAAAATCAGCATGGTGAACTATCCAAAAAGAAAGAAAAAA
TCTTATTATATTCAAACAAAAATACTCAAAATAAAAGCTTGAGAAAA

>g11500.t9 Gene=g11500 Length=413
MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSDKMPWFKGWAIERKEGKADGKCLIDALDAILPPQL
KSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDSKSSPPRGAADFTAQVIVLNH
PGQIANGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKAIKSGDAAIVNLVPSKP
LCVESFSEFPPLGRFAVRDMRQTVAVGVIKAVNFKEASGGKVTKAAEKAAKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g11500.t9 CDD cd01883 EF1_alpha 9 239 3.51984E-161
19 g11500.t9 CDD cd03705 EF1_alpha_III 286 389 2.04433E-73
15 g11500.t9 Gene3D G3DSA:3.40.50.300 - 1 234 1.5E-94
17 g11500.t9 Gene3D G3DSA:2.40.30.10 Translation factors 235 283 3.4E-14
16 g11500.t9 Gene3D G3DSA:2.40.30.10 Translation factors 286 393 9.3E-52
4 g11500.t9 PANTHER PTHR23115 TRANSLATION FACTOR 1 238 0.0
6 g11500.t9 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 238 0.0
3 g11500.t9 PANTHER PTHR23115 TRANSLATION FACTOR 240 410 0.0
5 g11500.t9 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 240 410 0.0
9 g11500.t9 PRINTS PR00315 GTP-binding elongation factor signature 9 22 1.3E-24
11 g11500.t9 PRINTS PR00315 GTP-binding elongation factor signature 68 76 1.3E-24
10 g11500.t9 PRINTS PR00315 GTP-binding elongation factor signature 88 98 1.3E-24
7 g11500.t9 PRINTS PR00315 GTP-binding elongation factor signature 104 115 1.3E-24
8 g11500.t9 PRINTS PR00315 GTP-binding elongation factor signature 148 157 1.3E-24
2 g11500.t9 Pfam PF00009 Elongation factor Tu GTP binding domain 5 236 5.5E-54
1 g11500.t9 Pfam PF03143 Elongation factor Tu C-terminal domain 287 392 1.1E-32
20 g11500.t9 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
21 g11500.t9 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 240 60.801
13 g11500.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 228 3.06E-76
14 g11500.t9 SUPERFAMILY SSF50447 Translation proteins 239 285 4.08E-9
12 g11500.t9 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 289 392 1.11E-44

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005525 GTP binding MF
GO:0003924 GTPase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values